example_pathfindR_output_clustered: Example Output for the pathfindR Clustering Workflow -...

In pathfindR.data: Data Package for 'pathfindR'

Example Output for the pathfindR Clustering Workflow - Rheumatoid Arthritis

Description

A dataset containing the results of pathfindR's clustering and partitioning workflow performed on the rheumatoid arthritis enrichment results example_pathfindR_output. The clustering and partitioning function cluster_enriched_terms was used with the default settings (i.e. hierarchical clustering was performed and the agglomeration method was "average"). Generated on Dec, 2022.

Usage

example_pathfindR_output_clustered

Format

A data frame with 128 rows and 11 columns:

ID

ID of the enriched term

Term_Description

Description of the enriched term

Fold_Enrichment

Fold enrichment value for the enriched term

occurrence

the number of iterations that the given term was found to enriched over all iterations

support

the median support (proportion of active subnetworks leading to enrichment within an iteration) over all iterations

s

lowest_p

the lowest adjusted-p value of the given term over all iterations

highest_p

the highest adjusted-p value of the given term over all iterations

Up_regulated

the up-regulated genes in the input involved in the given term, comma-separated

Down_regulated

the down-regulated genes in the input involved in the given term, comma-separated

Cluster

the cluster to which the enriched term is assigned

Status

whether the enriched term is the "Representative" term in its cluster or only a "Member"

See Also

example_pathfindR_input for the RA differentially-expressed genes data frame example_experiment_matrix for the RA differentially-expressed genes expression matrix run_pathfindR for details on the pathfindR enrichment analysis example_pathfindR_output for the RA example pathfindR enrichment output cluster_enriched_terms for details on clustering methods

pathfindR.data documentation built on April 27, 2023, 9:07 a.m.